Tokyo in the winter is kind of a waste of money.
Though I guess that goes for anywhere in Japan (bar Hokkaido).
Is it? Basically everything you can do in the summer you can do in winter, too, as far as I've noticed. A few places might close an hour or two earlier I think, and I guess Yoyogi park wouldn't be as lively (and therefore loses half the fun), but other than that, most things to do are equally fun to do. Just wrap up warm. I can confirm that Hokkaido is awesome in the winter, though, as you say. Probably more fun than it would be in any other season.
Also, since you're in the area, come visit Yokohama some time! The area around Minato Mirai, Sakuragichou, and Kannai is really nice, especially at night. And if you have enough time, making a day trip out to Kamakura (I think you can go direct from Tokyo on the Shounan-Shinjuku line) is recommended too. 
I've been to Minato Mirai and Kamakura! I was there in the day time, though. (According to my notes, we took the JR-Yokosuka line from Shinagawa to Kamakura, about 45 minutes and 690 yen.) IMO, you need more than a day to see Kamakura; it's easy to lose hours exploring the various temples.
Odaiba is another place that's cool to visit at night.
Oh yeah, now you mention it, I think you might be right - it might well be the Yokosuka line. I always get the various JR lines confused. And I also agree, I've spent two whole days there and only seen half the things I wanted to (and not all of them in as much detail as I'd have liked, either). And that's not even including Enoshima, which is right nearby and has a bunch more stuff to do. Some of the best bits are really well hidden away too, so you need to properly explore if you want to see everything. There's a really beautiful shrine hidden on a hill deep behind Kenchouji, which we'd never have even
noticed if we hadn't spent ages exploring every interesting-looking path in the main temple.
Minato Mirai looks a bit dull during the daytime, IMO. All the big buildings are mostly grey. But at night when they're all lit up, they have a totally different atmosphere to them. Although I agree, Odaiba is really, really nice too. I've only been there once, but it just so happened that they were doing a fireworks display that night, so we were able to have dinner on the balcony of a nice Italian restaurant and watch the fireworks over rainbow bridge while we ate. It was really nice.
